#1 This advantage is mitigated by the fact that the defender can support himself and chose the countering formation plus shield regeneration. With regeneration of the shield and repair of armor the first shot is not that valuable. Simultaneously shooting would make it much harder to have the battle visualised as an animation in rounds/steps. (Prototype of a battle replay: https://nc-client.jarunik.com/replay/M-ZTX2I0J1QS0)
#2 This would complicate battle significantly. Calculating every single ship is currently very costly to implement, very performance consuming for our server and much harder to balance. We would also need some form form of area damage or piercing as high damage ships would waste a lot of DPS on very small ships which would completely destroy balancing. So overall I currently don't see enough benefit for the costs to change that. I would love to implement a really sophisticated battle logic some day.
#3 I agree that this simplification does not reflect reality but I don't think we will ever aim to do realistic 3D modelling in our game. I agree with your judgement. A complete overhaul is not feasible as of now. We did discuss some different targeting and damage types like area damage but discarded it due to the involved efforts to design it in a balanced way. Would be cool to be able to do some more fancy battle module some day.
#4 We implemented abort due to the repeated requests of the community. We will monitor how it develops. We discussed the drawbacks of aborting but decided against some hard to understand timers/limits. One of our idea is to bring some features to allow sieges to planet to allow to reduce the options of constantly evading any fights due to clever ship logistics. We didn't decide on any feature or changes to abort yet though.
#5 The uranium refund was a quick fix to prevent stuck ships due to missing uranium for the return flight. It is not a feature and only happens due to some rounding and calculation problem. It is always a minimal amount and we intend to build a better solution for this longer term. We generally try to avoid passive protection without costs. If we would bring something like docking it would need a significant "fee" to provide absolute protection.
RE: The flaws in nextcolony's battle mechanistics and some suggestions to fix them.